Install Adore-Doris Error

[Khuram Shehzad]

Dear Members
I am using Ubuntu 14.04 LTS
I have installed GMT, SNAPHU, GETORB and DORIS. Doris installation only install bin, SAR Tools commands ENVISAT Tools and scr folder commands not installed. ENVISAT Tools and SCR directory command of DORIS are needed for ADORE-DORIS?. Sudo apt-get install adore-doris not working as described on wiki page. I manually put adore-doris-master in opt/adore and put the folder path of scr directory and i am not able to run commands in sub folder of scr directory I can run command adore but cannot run m_readfiles. when I put all of the sub folder commands in one folder then I can run each command. The problem is when i follow the tutorial and run adore -i it do not show setting file is missing but it shows the path of the scr directory. Please see attachments and please help how to install correctly if I am wrong. Can we run each command separately (m_readfiles, m_crop) out of adore shell? I am not able to run ADORE shell in terminal. Thanks

[Batuhan Osmanoglu]

Hello Khuram, 

Please reply-to adore...@googlegroups.com address so others can get your emails as well. 

There is something wrong with the adore setup. When you run "adore -i" you should get messages like this:

~$ adore -i

ADORESCR=/d2/home/bosmanoglu/codes/adore-doris/scr

User settings file is not defined. Using defaults.

projectFolder is set to ".". Use with caution.

Please set dataFolder or run: settings init.

runName is set to "default"

Any batch processing results (baselines, scripts with .adr ending) will be created under ./process/default

!ADORE:

If you don't get the ADORE: prompt at the end, you are not running ADORE. 

Can you send the output of the commands :
which adore

cat `which adore`

ls -l `which adore`

Make sure you use backquote (`) and not single quote (') for the above commands. 

Best, 

batu. 

On Thu, Nov 3, 2016 at 1:41 PM, Khuram Shehzad <ksheh...@gmail.com> wrote:

Dear Batu

Thank you very much for your quick response, I have checked doris and it is running now. I put the path for adore as you said and adore -i is running as well but the problem is I cannot follow the tutorial to process sample data as it is written in the tutorial available at http://www.osmanoglu.org/supplement/adore-doris-downloads/tutorial.pdf page 5 when you enter adore -i you will get message "user settings file is not defined......." I am not getting this message but when I enter adore - i I get

root@khuram-Inspiron-N5110:~# adore -i
ADORESCR=/opt/adore
root@khuram-Inspiron-N5110:~#

also when I enter command settings I am not getting any of command settings. when I enter settings I get this

root@khuram-Inspiron-N5110:~# settings
No command 'settings' found, did you mean:
Command 'gsettings' from package 'libglib2.0-bin' (main)
settings: command not found
root@khuram-Inspiron-N5110:~#

scr directory is set in the path

root@khuram-Inspiron-N5110:~# echo $PATH
/usr/local/GMT5SAR/bin:/usr/lib/doris:/opt/adore/scr:/usr/local/GMT5SAR/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
root@khuram-Inspiron-N5110:~#

Kindly help so that I can process sample data and follow the tutorial

Best Regards

Khuram Shehzad

On Thu, Nov 3, 2016 at 8:49 PM, Batuhan Osmanoglu <batuhan....@gmail.com> wrote:

Hello Khuram, 

ADORE itself does not need compilation therefore it can be copied anywhere on the computer. The "adore" executable has to be located in the path so that you can run "adore -i" etc... Once ADORE runs, it is setup to find where it is located on the computer, assume that is the ADORESCR (scripts) folder and set the path accordingly. 

For example I have the following lines in my .bashrc file for ADORE on Ubuntu 16.04:

export ADORESCR=/d2/home/bosmanoglu/codes/adore-doris/scr

export PATH=${PATH}:${ADORESCR}

export PATH=${PATH}:/opt/gmt/bin/

Make sure you have the ADORESCR in the path:

~$ echo $PATH

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/d2/home/bosmanoglu/codes/adore-doris/scr:/opt/gmt/bin/

Then you should be able to "adore -i"

External software like DORIS etc. needs to be in the path.  I had doris installed using the apt package. It should provide you the stuff to read envisat files etc (here is the code showing that envisat_dump_data is provided by package doris):

$ apt-file search envisat_dump_data

doris: /usr/lib/doris/envisat_dump_data

All the best, 

batu. 

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[Khuram Shehzad]

Hi Batu

Yes I am not getting ADORE prompt at the end I have downloaded the setup from
 https://github.com/bosmanoglu/adore-doris and extract in /opt/adore and set the path of scr directory

The output of the command which adore is

root@khuram-Inspiron-N5110:~# which adore
/opt/adore/scr/adore
root@khuram-Inspiron-N5110:~#

The output of command cat `which adore` is

root@khuram-Inspiron-N5110:~# cat `which adore`
#!/bin/bash
# ADORE
# Automatic Doris Environment
#
# USAGE:
#     adore adoreCommand
#    adore -u user.set adoreCommand
#    adore -u user.set -p dorisProcess
#    adore -u user.set -p dorisProcess adoreCommand
#    adore -v -p dorisProcess -d "adoreVariable1=Value1;adoreVariable2=Value2"
#    adore -i
#    adore -g
#    adore -V
#
# DESCRIPTION:
#    ADORE is an attempt to simplify processing of different interferometric stacks
#  like, single-master-stack, or short-baselines.
# default options are loaded from ${ADOREFOLDER}/set/default.set
# each doris step can be run. They should have a corresponding *.drs file in the drs folder.
#
# INPUT:
#  adoreCommand: see the manual for available adoreCommands
#  -u: user settings file.
#  -p: process Doris step. (m_readfiles, s_readfiles, interfero...)
#  -d: define variable (has priority over user settings file.)
#  -i: open interactive session.
#  -g: flag for ADORE-GUI. This is useless if you are not using ADORE-GUI.
#  -v: verbose. For troubleshooting. Equivalent to: set -x
#  -V: Version. Print ADORE version and exit.
#
# if both adoreCommand and dorisProcess is used, first the dorisProcess
# is run, and then the adoreCommand.
#
# OUTPUT:
#  nothing for adoreCommands.
#  dorisStep: SUCCESS for successful doris processing steps.
#

#NOT NECESSARY WITH CHILD BASH PROCESS
#ctrl_c()
#{
## if [ "${ctrl_c_counter-0}" -lt "1" ]; then
#   #ctrl_c_counter=`expr ${ctrl_c_counter} + 1`
#   #bind redraw-current-line  
#   echo -n "^C"
#   continue
#   #return 0
## else
##   echo " "
##   echo "Saving History..."
##   history -w ${adoreHistoryFile}
##   exit 0;
## fi
#}

if [ "${1-allEmpty}" == "allEmpty" ]; then
  sed -n -e '/^# USAGE:/,/^$/ s/^# \?//p' < ${0}
  exit 0
fi


###### GET INPUT OPTIONS
#start a loop for getopts. I want to read parameters of options -n -i  etc.
while getopts  "givVu:p:d:" flag
do
  #echo "$flag" $OPTIND $OPTARG
  # above line outputs the parameter flag (-n, etc.),
  #index of the flag in the commandline and  the argument. If you just want
  #a flag then you simply remove the column from getopts line
  #(i.e. to make n a flag "ni:a:...")
  eval export ${flag}=${OPTARG}
done
# now $u=userSettings, $p=dorisProcess, $d=defineVariables
#below I use a for loop to remove already parsed parameters
for ((k=1; k<$OPTIND; k++ ))
do
  shift
done
unset flag OPTARG OPTIND
if [ "${v-notVerbose}" != "notVerbose" ]; then
  set -x
fi

# now I can assign values to the leftover parameters.
# Need to export the variables to make them available in interactive subshell
export adoreCommand=$1
export dorisProcess=$p

if [ "${ADORESCR:-isEmpty}" = "isEmpty" ]; then
  #Two methods to find ADORE path
  #LSOF is capable of following links. But not available on all systems
  #dirname method can not follow links causing trouble when adore is a link.
  LSOF=$(lsof -p $$ | grep -E "/"$(basename $0)"$") # get the location of running script
  if [ $? -ne 0 ]; then
   ADORESCR=`echo $(cd $(dirname ${0}); pwd -P)`
   if [ -d ${ADORESCR}/fun ]; then
     export ADORESCR
   else
     echo "ADORE could not define ADORESCR. Please set it as environment variable and retry. ex: export ADORESCR=/opt/adore/scr"
     exit
   fi
  else
    export ADORESCR=$(dirname ${LSOF##* })
  fi
fi
echo ADORESCR=${ADORESCR}
#adjust path in /ADORESCR/.adore.rc, only if interactive
export _ADOREPATH=${PATH}:${ADORESCR}
if [ "${V-printVersion}" != "printVersion" ]; then
  echo "Version=$(cat ${ADORESCR}/../version )"
  exit
fi

if [ "${i-notInteractive}" != "notInteractive" ]; then
  #interactive - start shell
  bash --init-file "${ADORESCR}/.adore.rc"
#  set -o emacs
#  set -o histexpand
#  HISTCONTROL=ignoreboth
#  #set bind-tty-special-chars off
#  #bind TAB:complete
#  #bind '"TAB":complete-variable'
#  #bind '"M-[A":history-search-backward'
#  #bind '"M-[B":history-search-forward'
#  #ctrl-r is reverse search history... bind Control-r:redraw-current-line
#  #adoreHistoryFile=${ADOREFOLDER}/scr/.history
#  #INPUTRC=${ADOREFOLDER}/scr/.inputrc
#  [ -e "/etc/bash_completion" ] && source /etc/bash_completion
#  [ -e "${ADOREFOLDER}/scr/.inputrc" ] && source ${ADOREFOLDER}/scr/.inputrc
# #  bind -f ${ADOREFOLDER}/scr/.bind
#
#  history -r ${adoreHistoryFile}
#  while [ 1 ]; do
#    #PS1='ADORE: '
#    #echo -n "ADORE: "
#    #ctrl_c_counter_bck=${ctrl_c_counter}
#    read -r -p "ADORE: " -e command
#    [ -n "${command}" ] && history -s "${command}"  #add command to history if not empty
#    #echo TEST: ${command%% *} #get the first word.
#    case "${command%% *}" in
#      exit)
#        history -w ${adoreHistoryFile} #save history
#        exit 0
#        ;;
#      \?)
#        if [ "${command#* }" == "?" ]; then
#          sed -n -e '/^# USAGE:/,/^$/ s/^# \?//p' < "${ADORESCR}/fun/?"
#          continue;
#        fi
#        h ${command#* }    
#        ;;
#      *)
#        eval ${command}
#        ;;
#    esac
#    #I'm placing the trap counter in the loop
#    #so that if a script changes the trap, when
#    #we are back to adore it goes back to ADORE's trap.
#    #trap ctrl-c and call ctrl_c()
#    trap ctrl_c 2 # ctrl+c=sigint 2
#  done
else
  #not interactive - batch processing
  source ${ADORESCR}/.adore.rc
fi

exit 0
root@khuram-Inspiron-N5110:~#

The output of the command  ls -l `which adore` is

root@khuram-Inspiron-N5110:~# ls -l `which adore`
-rwxrwxr-x 1 root root 5234 جنوري 22  2012 /opt/adore/scr/adore
root@khuram-Inspiron-N5110:~#

Thanks

Khuram

 

[Batuhan Osmanoglu]

OK, 

Seems like something is wrong and ADORESCR is not being detected correctly. You can set it manually by:

export ADORESCR=/opt/adore/scr

Then try to restart adore with -i. It "should" work. If not try to use the pre-installed DVD. 

http://www.osmanoglu.org/sar/98-live-dvd-for-adore-doris

Best, 

batu. 

[Khuram Shehzad]

Thank you for great help I exported manually now I am getting adore prompt at the end. Now will try to process sample data will post if any errors. thanks a lot

[DavePoreh]

Ciao Batu, 

I read that you might not be able to answer the posts!!! (even might be this post)... and that is not good for us:(

Just as a reminder : Still sudo apt-get install adore-doris does  not work.

If you have your web page, I think you could do something...

All the best wishes with your life and really really thank you for everything :)

Cheers, 

Dave

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